Contacts of the helix formed by residues 235 - 245 (chain A) in PDB entry 2A7P
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A LEU* 3.8 2.4 - - - +
234A LEU* 1.3 81.8 + - - +
236A ALA* 1.3 63.7 + - - +
237A GLU* 3.7 14.5 + - - +
238A ASP* 3.0 31.9 + - - +
239A ALA* 3.0 19.9 + - - +
252A LEU* 4.7 1.0 - - - +
269A VAL* 4.0 11.1 - - - +
273A SER* 4.0 4.3 - - - -
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Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A SER* 1.3 71.6 - - - +
237A GLU* 1.3 60.2 + - - +
239A ALA* 3.3 2.3 + - - +
240A ASP* 2.9 30.7 + - - +
269A VAL* 4.5 4.4 - - - +
272A GLN* 3.6 40.7 - - + +
273A SER* 3.3 30.8 + - - +
276A LYS* 3.7 16.3 - - + +
277A THR* 4.7 1.0 - - - +
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Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A SER* 3.1 12.7 - - - +
236A ALA* 1.3 84.4 + - - +
238A ASP* 1.3 64.6 + - - +
240A ASP* 3.2 7.3 + - - +
241A ARG* 3.0 22.2 + - - +
272A GLN* 3.7 19.8 + - - +
276A LYS* 3.7 16.1 + - - -
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Residues in contact with ASP 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A TRP* 3.8 21.0 - - + -
233A LEU* 3.9 24.6 - - + +
234A LEU 5.3 2.5 + - - +
235A SER* 3.0 23.4 + - - +
237A GLU* 1.3 76.2 - - - +
239A ALA* 1.3 64.8 + - - +
241A ARG* 3.3 6.2 + - - +
242A CYS* 3.0 27.5 + - - -
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Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU* 3.4 21.7 - - + +
235A SER 3.0 12.6 + - - +
236A ALA 3.6 8.5 - - - +
238A ASP* 1.3 76.8 - - - +
240A ASP* 1.3 62.0 + - - +
242A CYS* 3.3 4.5 + - - +
243A ILE* 3.2 25.8 + - - +
250A VAL* 3.9 15.2 - - + +
252A LEU* 4.6 3.1 - - + -
273A SER* 4.3 11.2 - - - +
277A THR* 3.7 17.3 - - + -
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Residues in contact with ASP 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ALA 2.9 17.6 + - - +
237A GLU* 3.5 5.6 - - - +
239A ALA* 1.3 74.9 - - - +
241A ARG* 1.3 60.1 + - - +
243A ILE* 3.2 7.5 + - - +
244A ALA* 3.0 27.8 + - - +
276A LYS* 3.3 44.8 - - + +
277A THR* 3.7 12.7 - - + +
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Residues in contact with ARG 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A TRP* 3.3 69.5 - - + +
218A ARG* 4.1 6.9 - - - +
237A GLU 3.0 12.6 + - - +
238A ASP* 3.6 9.9 - - - +
239A ALA 3.3 0.2 - - - -
240A ASP* 1.3 72.5 - - - +
242A CYS* 1.3 61.7 + - - +
244A ALA* 2.9 11.3 + - - +
245A GLU* 2.8 54.7 + - - +
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Residues in contact with CYS 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A TRP* 3.7 23.1 - - - -
217A LEU* 4.5 3.0 - - - +
230A VAL* 3.7 26.9 - - + -
233A LEU* 3.6 20.2 - - - -
238A ASP 3.0 20.6 + - - -
239A ALA 3.4 9.0 - - - +
241A ARG* 1.3 76.5 - - - +
243A ILE* 1.3 59.9 + - - +
245A GLU* 3.2 10.4 + - - +
246A GLY 3.3 0.7 + - - -
247A ALA* 2.9 34.0 + - + +
250A VAL* 3.9 13.7 - - + -
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Residues in contact with ILE 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ALA 3.2 16.3 + - - +
240A ASP* 3.5 9.2 - - - +
241A ARG 3.2 0.4 - - - -
242A CYS* 1.3 76.3 - - - +
244A ALA* 1.3 63.7 + - - +
246A GLY* 3.1 14.7 + - - -
247A ALA 3.7 21.4 - - - +
249A GLY* 4.1 18.2 - - - +
250A VAL* 4.2 9.9 - - + -
277A THR* 4.0 24.7 - - - +
279A LYS* 3.6 37.0 - - + -
280A PRO 5.4 0.4 - - - +
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Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ASP* 3.0 14.6 + - - +
241A ARG* 2.9 19.4 + - - +
243A ILE* 1.3 77.9 - - - +
245A GLU* 1.3 62.6 + - + +
246A GLY 3.3 0.7 + - - -
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Residues in contact with GLU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A TRP* 4.0 15.8 - - + +
217A LEU* 3.9 21.4 - - + +
218A ARG* 2.6 60.4 + - + +
221A ARG* 4.1 16.1 - - - +
241A ARG* 2.8 43.4 + - - +
242A CYS 3.2 5.8 + - - +
243A ILE 3.1 0.4 - - - -
244A ALA* 1.3 79.4 - - - +
246A GLY* 1.3 57.1 + - - +
247A ALA 3.8 0.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il